diff --git a/src/lib_gui/utility/utilityApp.cpp b/src/lib_gui/utility/utilityApp.cpp
index 2c7e287a..e548515d 100644
--- a/src/lib_gui/utility/utilityApp.cpp
+++ b/src/lib_gui/utility/utilityApp.cpp
@@ -147,11 +147,14 @@ int utility::executeProcessAndGetExitCode(
 	bool logProcessOutput,
 	std::wstring* errorMessage
 ){
+	bool finished = false;
+
 	QProcess process;
 
-	if (errorMessage != nullptr)
+	QObject::connect(&process, &QProcess::errorOccurred, [&finished, errorMessage, commandPath](QProcess::ProcessError error)
 	{
-		QObject::connect(&process, &QProcess::errorOccurred, [errorMessage, commandPath](QProcess::ProcessError error)
+		finished = true;
+		if (errorMessage != nullptr)
 		{
 			switch (error)
 			{
@@ -173,9 +176,15 @@ int utility::executeProcessAndGetExitCode(
 			case QProcess::UnknownError:
 				*errorMessage = L"An unknown error occurred while executing process.";
 				break;
-			};
-		});
-	}
+			}
+		};
+	});
+
+	QObject::connect(&process, static_cast<void(QProcess::*)(int, QProcess::ExitStatus)>(&QProcess::finished), [&finished](int exitCode, QProcess::ExitStatus exitStatus)
+	{
+		finished = true;
+	});
+
 
 	if (!workingDirectory.empty())
 	{
@@ -204,7 +213,7 @@ int utility::executeProcessAndGetExitCode(
 		std::wstring errorBuffer;
 		if (timeout == -1)
 		{
-			while (!process.waitForFinished(1000))
+			while (!finished && process.waitForFinished(1000))
 			{
 				if (logProcessOutput)
 				{
@@ -214,7 +223,10 @@ int utility::executeProcessAndGetExitCode(
 		}
 		else
 		{
-			process.waitForFinished(timeout);
+			if (!finished)
+			{
+				process.waitForFinished(timeout);
+			}
 		}
 
 		if (logProcessOutput)
diff --git a/testing/project_setup/cpp_empty_pch/data/src/Bar.h b/testing/project_setup/cpp_empty_pch/data/src/Bar.h
index 1cb93caf..4f95103a 100644
--- a/testing/project_setup/cpp_empty_pch/data/src/Bar.h
+++ b/testing/project_setup/cpp_empty_pch/data/src/Bar.h
@@ -1,5 +1,5 @@
-#ifndef FOO_H
-#define FOO_H
+#ifndef BAR_H
+#define BAR_H
 
 #include "FooBar.h"
 
@@ -7,4 +7,4 @@ class Bar : public FooBar
 {
 };
 
-#endif // FOO_H
+#endif // BAR_H
diff --git a/testing/project_setup/cpp_empty_pch/data/src/Foo.h b/testing/project_setup/cpp_empty_pch/data/src/Foo.h
index 1ad18563..75082486 100644
--- a/testing/project_setup/cpp_empty_pch/data/src/Foo.h
+++ b/testing/project_setup/cpp_empty_pch/data/src/Foo.h
@@ -1,5 +1,5 @@
-#ifndef BAR_H
-#define BAR_H
+#ifndef FOO_H
+#define FOO_H
 
 #include "FooBar.h"
 
@@ -7,4 +7,4 @@ class Foo : public FooBar
 {
 };
 
-#endif // FOO_BAR_H
+#endif // FOO_H
diff --git a/testing/project_setup/custom_command_python/checklist.txt b/testing/project_setup/custom_command_python/checklist.txt
index be4ab163..f379c002 100644
--- a/testing/project_setup/custom_command_python/checklist.txt
+++ b/testing/project_setup/custom_command_python/checklist.txt
@@ -10,7 +10,7 @@
 * Click "Add Source Group"
 * Select "Custom" -> "Custom Command Source Group"
 * Click "Next"
-* Add "python <path/to/working_copy>/SourcetrailPythonIndexer/run.py --source-file-path=%{SOURCE_FILE_PATH} --database-file-path=%{DATABASE_FILE_PATH}" to "Custom Command"
+* Add "python <path/to/working_copy>/SourcetrailPythonIndexer/run.py index --source-file-path=%{SOURCE_FILE_PATH} --database-file-path=%{DATABASE_FILE_PATH}" to "Custom Command"
 * Add "./src" to "Files & Directories to Index"
 * Add "**main*" to "Excluded Files & Directories"
 * Add ".py" to "Source File Extensions"
@@ -34,7 +34,7 @@
 * Click "Save"
 * Validate a project-file-was-changed-notification appears
 * Click "Reindex"
-* Validate "Updated files" is selected
+* Validate "All files" is selected
 * Validate "source files to index" shows "3"
 * Click "Updated files"
 * Validate "source files to index" shows "1"
@@ -43,7 +43,9 @@
 * Click "OK"
 * Validate content of code and graph view changed and display calls from "main"
 * Run "2_update.sh"
+* Click "Refresh" button
 * Validate "Updated files" is selected
+* Validate "files to clear" shows "1"
 * Validate "source files to index" shows "1"
 * Click Start
 * Validate a dialog appears that states that the project cannot be partially cleared
@@ -57,7 +59,8 @@
 * Validate "Warning appears that %{SOURCE_FILE_PATH} is not defined in command"
 * In "Custom Command" replace "foo" with "%{SOURCE_FILE_PATH}"
 * Click "Save"
-* Click "Refresh" button
+* Validate a project-file-was-changed-notification appears
+* Click "Reindex"
 * Click "Start"
 * Validate "Log View appears showing errors that command execution failed".
 * Close Sourcetrail